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BMRB: 36086

5XND

Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel

Authors

Kumeta, H., Nakayama, H., Ogura, K.

Assembly

Parvalbumin beta

Entity

1. Parvalbumin beta (polymer, Thiol state: all free), 114 monomers, 11956.44 Da Detail

GPLGSMAFAS VLKDAEVTAA LDGCKAAGSF DHKKFFKACG LSGKSTDEVK KAFAIIDQDK SGFIEEEELK LFLQNFKAGA RALSDAETKA FLKAGDSDGD GKIGIDEFAA MIKG

2. CALCIUM ION (non-polymer), 40.078 × 2 Da

Total weight

12036.597 Da

Max. entity weight

11956.44 Da

Entity Connection

metal coordination 12 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:ASP57:OD1	2:CA1:CA
2	metal coordination	sing	1:ASP59:OD1	2:CA1:CA
3	metal coordination	sing	1:SER61:OG	2:CA1:CA
4	metal coordination	sing	1:PHE63:O	2:CA1:CA
5	metal coordination	sing	1:GLU68:OE1	2:CA1:CA
6	metal coordination	sing	1:GLU68:OE2	2:CA1:CA
7	metal coordination	sing	1:ASP96:OD1	2:CA1:CA
8	metal coordination	sing	1:ASP98:OD1	2:CA1:CA
9	metal coordination	sing	1:ASP100:OD1	2:CA1:CA
10	metal coordination	sing	1:LYS102:O	2:CA1:CA
11	metal coordination	sing	1:GLU107:OE1	2:CA1:CA
12	metal coordination	sing	1:GLU107:OE2	2:CA1:CA

Source organism

Scomber japonicus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.5 %, Completeness: 94.2 %, Completeness (bb): 95.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.2 % (1196 of 1269)	96.0 % (629 of 655)	91.4 % (455 of 498)	96.6 % (112 of 116)
Backbone	95.9 % (654 of 682)	95.0 % (228 of 240)	96.4 % (317 of 329)	96.5 % (109 of 113)
Sidechain	93.2 % (641 of 688)	96.6 % (401 of 415)	87.8 % (237 of 270)	100.0 % (3 of 3)
Aromatic	72.1 % (75 of 104)	94.2 % (49 of 52)	50.0 % (26 of 52)
Methyl	96.5 % (110 of 114)	96.5 % (55 of 57)	96.5 % (55 of 57)

1. Parvalbumin beta

GPLGSMAFAS VLKDAEVTAA LDGCKAAGSF DHKKFFKACG LSGKSTDEVK KAFAIIDQDK SGFIEEEELK LFLQNFKAGA RALSDAETKA FLKAGDSDGD GKIGIDEFAA MIKG

Show sample condition

Sample

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-13C; U-15N] Sco j 1, 7 % [U-2H] D2O, 20 mM MES, 150 mM sodium chloride, 10 mM CaCl2, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.31 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.5 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5XND, Strand ID: A Detail

Release date

2017-08-29

Citation

Solution structure of the major fish allergen parvalbumin Sco j 1 derived from the Pacific mackerel
Kumeta, H., Nakayama, H., Ogura, K.
Sci. Rep. (2017), 7, 17160-17160, PubMed 29215073 , DOI 10.1038/s41598-017-17281-6 , Abstract

Related entities 1. Parvalbumin beta, : 1 : 1 : 144 entities Detail

Experiments performed 18 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 0.5 mM [U-13C; U-15N] Sco j 1, 7 % [U-2H] D2O, 20 mM MES, 150 mM sodium chloride, 10 mM CaCl2, 93% H2O/7% D2O

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

3 2D 1H-13C HSQC aromatic

Instrument

Varian UNITY - 500 MHz scorpio

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

4 3D HNCO

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

5 3D HN(CO)CA

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

6 3D HNCA

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

7 3D CBCA(CO)NH

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

8 3D HNCACB

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

9 3D C(CO)NH

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

10 3D HBHA(CO)NH

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

11 3D HN(CA)HA

Instrument

Varian UNITY - 600 MHz libra

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

12 3D 1H-15N NOESY

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

13 3D 3D HCCH-TOCSY aliphatic

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

14 3D 1H-13C NOESY aliphatic

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

15 2D HbCbCgCdHd

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

16 2D HbCbCgCdCeHe

Instrument

Bruker AvanceIII HD - 800 MHz migi

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

17 3D 1H-13C NOESY aromatic

Instrument

Varian UNITY - 500 MHz scorpio

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

18 3D HCCH-TOCSY aromatic

Instrument

Varian UNITY - 500 MHz scorpio

Sample

#	Name	Isotope labeling	Type	Concentration
1	Sco j 1	[U-13C; U-15N]	protein	0.5 mM
2	CaCl2	natural abundance	salt	10 mM
3	sodium chloride	natural abundance	salt	150 mM
4	MES	natural abundance	buffer	20 mM
5	H2O	natural abundance	solvent	93 %
6	D2O	[U-2H]	solvent	7 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_36086_5xnd.nef
Input source #2: Coordindates	5xnd.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:57:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:59:ASP:OD1	2:1:CA:CA	unknown	unknown	n/a
1:61:SER:OG	2:1:CA:CA	unknown	unknown	n/a
1:63:PHE:O	2:1:CA:CA	unknown	unknown	n/a
1:68:GLU:OE1	2:1:CA:CA	unknown	unknown	n/a
1:68:GLU:OE2	2:1:CA:CA	unknown	unknown	n/a
1:96:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:98:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:100:ASP:OD1	2:2:CA:CA	unknown	unknown	n/a
1:102:LYS:O	2:2:CA:CA	unknown	unknown	n/a
1:107:GLU:OE1	2:2:CA:CA	unknown	unknown	n/a
1:107:GLU:OE2	2:2:CA:CA	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	CA	CALCIUM ION	None
B	2	CA	CALCIUM ION	None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-------------10--------20--------30--------40--------50--------60--------70--------80--------90-----
GPLGSMAFASVLKDAEVTAALDGCKAAGSFDHKKFFKACGLSGKSTDEVKKAFAIIDQDKSGFIEEEELKLFLQNFKAGARALSDAETKAFLKAGDSDGD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSMAFASVLKDAEVTAALDGCKAAGSFDHKKFFKACGLSGKSTDEVKKAFAIIDQDKSGFIEEEELKLFLQNFKAGARALSDAETKAFLKAGDSDGD
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

--100---------
GKIGIDEFAAMIKG
||||||||||||||
GKIGIDEFAAMIKG
-------110----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0

Content subtype: combined_36086_5xnd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	12		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1203		96.5 (chain: A, length: 114)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2637 (1)	noe	95.6 (chain: A, length: 114)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	OK	1122 (1)	noe	90.4 (chain: A, length: 114)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	171 (171)	.	93.0 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 96.5%
- Total number of assignments
  - ¹H chemical shifts: 632
  - ¹³C chemical shifts: 458
  - ¹⁵N chemical shifts: 113
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
24	SER	HG	6.103
53	GLN	CD	179.625
69	GLN	CD	179.584
76	ARG	HH11	6.194
76	ARG	CZ	160.774
79	SER	HG	6.284

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	655	629	96.0
¹³C chemical shifts	498	455	91.4
¹⁵N chemical shifts	117	113	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	240	228	95.0
¹³C chemical shifts	228	218	95.6
¹⁵N chemical shifts	113	109	96.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	415	401	96.6
¹³C chemical shifts	270	237	87.8
¹⁵N chemical shifts	4	4	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	59	57	96.6
¹³C chemical shifts	59	57	96.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	52	49	94.2
¹³C chemical shifts	52	26	50.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 95.6%
- Total number of restraints: 2637
- Weight of restraints: 1.0 (2637)
- Potential type of restraints: upper-bound-parabolic (2637)
- Range of distance target values: 2.35, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 90.4%
  - Total number of restraints: 1122
  - Weight of restraints: 1.0 (1122)
  - Potential type of restraints: upper-bound-parabolic (1122)
  - Range of distance target values: 6.0, 6.0 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 93.0%
- Total number of restraints: 171
- Total number of restraints per polymer type: 171
- Weight of restraints: 1.0 (171)
- Potential type of restraints: square-well-parabolic (171)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords STRUCTURE FROM CYANA 2.1

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Found 1 Document (0.877 seconds)

BMRB: 36086

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Parvalbumin beta, : 1 : 1 : 144 entities Detail

Experiments performed 18 experiments Detail

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NMR combined restraints 5 contents Detail